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Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 25% (w/v) PEG 3350, 0.1 M Tris, pH 8.5 and 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.99 38.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.71 α = 90 b = 97.036 β = 111.83 c = 84.215 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97933 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 50 98.6 0.082 0.082 3.7 70428
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 97.4 0.362 0.362 4.81 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.95 50 66826 3545 98.49 0.15897 0.15631 0.1635 0.20916 0.2139 RANDOM 26.35
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.01 -0.55 0.08 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.617 r_dihedral_angle_4_deg 18.201 r_dihedral_angle_3_deg 16.201 r_long_range_B_refined 7.446 r_long_range_B_other 7.065 r_dihedral_angle_1_deg 5.803 r_scangle_other 5.017 r_mcangle_it 3.409 r_mcangle_other 3.409 r_scbond_it 3.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.617 r_dihedral_angle_4_deg 18.201 r_dihedral_angle_3_deg 16.201 r_long_range_B_refined 7.446 r_long_range_B_other 7.065 r_dihedral_angle_1_deg 5.803 r_scangle_other 5.017 r_mcangle_it 3.409 r_mcangle_other 3.409 r_scbond_it 3.393 r_scbond_other 3.392 r_mcbond_it 2.405 r_mcbond_other 2.405 r_angle_refined_deg 2.028 r_angle_other_deg 0.895 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7286 Nucleic Acid Atoms Solvent Atoms 610 Heterogen Atoms 148
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling